Retire `make_afun()` - Batch 2 #1392

edelarua · 2025-02-19T17:38:19Z

Pull Request

Fixes #1382

github-actions · 2025-02-19T17:48:32Z

Unit Tests Summary

1 files 84 suites 1m 18s ⏱️
878 tests 869 ✅ 9 💤 0 ❌
1 888 runs 1 191 ✅ 697 💤 0 ❌

Results for commit 8cefbde.

♻️ This comment has been updated with latest results.

github-actions · 2025-02-19T17:48:38Z

Unit Test Performance Difference

Test Suite	$Status$	Time on `main`	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
analyze_vars_in_cols	💔	$2.23$	$+3.47$	$+17$	$-7$	$0$	$0$
count_occurrences	💔	$0.76$	$+1.60$	$+10$	$-8$	$0$	$0$
summarize_coxreg	💔	$3.38$	$+1.83$	$+13$	$-13$	$0$	$0$
summarize_num_patients	💔	$1.12$	$+1.22$	$+18$	$-16$	$0$	$0$
survival_duration_subgroups	💔	$4.64$	$+1.33$	$+7$	$-14$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on `main`	$±Time$	Test Case
analyze_vars_in_cols	💔	$0.46$	$+1.53$	summarize_works_with_nested_analyze

Results for commit f583fac

♻️ This comment has been updated with latest results.

github-actions · 2025-02-19T17:50:39Z

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      96       3  96.88%   235, 237-238
R/abnormal_by_marked.R                        83       8  90.36%   94-98, 274, 276-277
R/abnormal_by_worst_grade.R                   89       3  96.63%   208, 210-211
R/abnormal_lab_worsen_by_baseline.R          150      10  93.33%   194-197, 202, 204-205, 448-450
R/abnormal.R                                  73       2  97.26%   215, 217
R/analyze_variables.R                        287       5  98.26%   587-590, 778
R/analyze_vars_in_cols.R                     178      14  92.13%   178, 221, 235-236, 238, 246-254
R/bland_altman.R                              92       1  98.91%   46
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                         35       0  100.00%
R/control_incidence_rate.R                    10       0  100.00%
R/control_logistic.R                           7       0  100.00%
R/control_step.R                              23       1  95.65%   58
R/control_survival.R                          15       0  100.00%
R/count_cumulative.R                          59       1  98.31%   74
R/count_missed_doses.R                        36       0  100.00%
R/count_occurrences_by_grade.R               153       2  98.69%   177, 272
R/count_occurrences.R                        115       1  99.13%   118
R/count_patients_events_in_cols.R             67       1  98.51%   60
R/count_patients_with_event.R                 61       1  98.36%   123
R/count_patients_with_flags.R                 84       1  98.81%   137
R/count_values.R                              68       2  97.06%   206, 209
R/cox_regression_inter.R                     154       0  100.00%
R/cox_regression.R                           161       0  100.00%
R/coxph.R                                    167       7  95.81%   191-195, 238, 253, 261, 267-268
R/d_pkparam.R                                406       0  100.00%
R/decorate_grob.R                            113       0  100.00%
R/desctools_binom_diff.R                     621      64  89.69%   53, 88-89, 125-126, 129, 199, 223-232, 264, 266, 286, 290, 294, 298, 353, 356, 359, 362, 422, 430, 439, 444-447, 454, 457, 466, 469, 516-517, 519-520, 522-523, 525-526, 593, 604-616, 620, 663, 676, 680
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  50       1  98.00%   65
R/estimate_proportion.R                      205      11  94.63%   83-90, 94, 99, 320, 486
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/formatting_functions.R                     183       2  98.91%   141, 276
R/g_forest.R                                 585      60  89.74%   240, 252-255, 260-261, 275, 277, 287-290, 335-338, 345, 414, 501, 514, 518-519, 524-525, 538, 554, 601, 630, 705, 714, 720, 739, 794-814, 817, 828, 847, 902, 905, 1040-1045
R/g_ipp.R                                    133       0  100.00%
R/g_km.R                                     350      57  83.71%   285-288, 307-309, 363-366, 400, 428, 432-475, 482-486
R/g_lineplot.R                               260      22  91.54%   204, 378-385, 424-434, 543, 551
R/g_step.R                                    68       1  98.53%   108
R/g_waterfall.R                               47       0  100.00%
R/h_adsl_adlb_merge_using_worst_flag.R        73       0  100.00%
R/h_biomarkers_subgroups.R                    46       0  100.00%
R/h_cox_regression.R                         110       0  100.00%
R/h_incidence_rate.R                          45       0  100.00%
R/h_km.R                                     509      41  91.94%   137, 189-194, 287, 378, 380-381, 392-394, 413, 420-421, 423-425, 433-435, 460, 465-468, 651-654, 1108-1119
R/h_logistic_regression.R                    468       3  99.36%   203-204, 273
R/h_map_for_count_abnormal.R                  54       0  100.00%
R/h_pkparam_sort.R                            15       0  100.00%
R/h_response_biomarkers_subgroups.R           90      12  86.67%   50-55, 107-112
R/h_response_subgroups.R                     178      18  89.89%   257-270, 329-334
R/h_stack_by_baskets.R                        64       1  98.44%   89
R/h_step.R                                   180       0  100.00%
R/h_survival_biomarkers_subgroups.R           88       6  93.18%   111-116
R/h_survival_duration_subgroups.R            207      18  91.30%   259-271, 336-341
R/imputation_rule.R                           17       0  100.00%
R/incidence_rate.R                            86       7  91.86%   67-72, 152
R/logistic_regression.R                      102       0  100.00%
R/missing_data.R                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               117       0  100.00%
R/prop_diff_test.R                            91       0  100.00%
R/prop_diff.R                                265      15  94.34%   70-73, 105, 290-297, 440, 605
R/prune_occurrences.R                         57       0  100.00%
R/response_biomarkers_subgroups.R             69       6  91.30%   196-201
R/response_subgroups.R                       214       8  96.26%   100-105, 260-261
R/riskdiff.R                                  65       5  92.31%   102-105, 114
R/rtables_access.R                            38       0  100.00%
R/score_occurrences.R                         20       1  95.00%   124
R/split_cols_by_groups.R                      49       0  100.00%
R/stat.R                                      59       0  100.00%
R/summarize_ancova.R                         139       2  98.56%   313-314
R/summarize_change.R                          77       1  98.70%   189
R/summarize_colvars.R                         10       0  100.00%
R/summarize_coxreg.R                         172       0  100.00%
R/summarize_glm_count.R                      266      10  96.24%   129-130, 202-203, 456-460, 593
R/summarize_num_patients.R                    93       4  95.70%   117-119, 266
R/summarize_patients_exposure_in_cols.R       96       1  98.96%   56
R/survival_biomarkers_subgroups.R             78       6  92.31%   117-122
R/survival_coxph_pairwise.R                   84      12  85.71%   51-52, 64-73
R/survival_duration_subgroups.R              212       6  97.17%   124-129
R/survival_time.R                            111       0  100.00%
R/survival_timepoint.R                       124      10  91.94%   131-140
R/utils_checkmate.R                           68       0  100.00%
R/utils_default_stats_formats_labels.R       178       0  100.00%
R/utils_factor.R                              87       1  98.85%   84
R/utils_ggplot.R                             110       0  100.00%
R/utils_grid.R                               126       5  96.03%   164, 279-286
R/utils_rtables.R                            124       9  92.74%   39, 46, 403-404, 526-530
R/utils_split_funs.R                          52       2  96.15%   82, 94
R/utils.R                                    141       7  95.04%   118, 121, 124, 128, 137-138, 332
TOTAL                                      11140     501  95.50%

Diff against main

Filename                   Stmts    Miss  Cover
-----------------------  -------  ------  -------
R/summarize_ancova.R         +33       0  +0.45%
R/summarize_glm_count.R      +28      +2  -0.40%
TOTAL                        +61      +2  +0.01%

Results for commit: 8cefbde

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

shajoezhu · 2025-02-20T01:22:50Z

all looks good downstream in scda.test insightsengineering/scda.test#187

…82_retire_make_afun_2

R/summarize_ancova.R

Melkiades

Lgtm! Why no custom stats for this one? is it because it uses a summary output? Anyway we can come back to it later. Thanks Emily!!

Melkiades · 2025-02-25T08:55:10Z

R/summarize_ancova.R

@@ -232,7 +237,7 @@ a_ancova <- function(df,
  )

  # Fill in formatting defaults
-  .stats <- get_stats("summarize_ancova", stats_in = .stats)
+  .stats <- c(get_stats("summarize_ancova", stats_in = .stats), names(custom_stat_functions))


This forces the order. I have a fix ready, I will add it in another PR ;)

edelarua added 5 commits February 19, 2025 12:15

Update summarize_glm_count

0bc6880

Update NEWS

5cf1aad

Defaults

5c27ade

Update summarize_ancova

f17c25f

Clean up

c5cc9d0

edelarua added the sme label Feb 19, 2025

Update docs

495f2ea

edelarua and others added 3 commits February 19, 2025 19:36

Don't need levels_per_stats

3816743

[skip style] [skip vbump] Restyle files

64a60c0

Clean up defaults

75f62cb

shajoezhu and others added 4 commits February 20, 2025 09:23

Empty-Commit

054a7bd

Merge remote-tracking branch 'origin/1382_retire_make_afun_2' into 13…

73eb04c

…82_retire_make_afun_2

[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

28ec869

Fix lint

cc6803f

Melkiades reviewed Feb 21, 2025

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R/summarize_ancova.R Outdated Show resolved Hide resolved

Merge branch 'main' into 1382_retire_make_afun_2

d97de73

Melkiades approved these changes Feb 24, 2025

View reviewed changes

edelarua added 2 commits February 24, 2025 15:17

Re-add custom stat function option

54a711a

Merge branch 'main' into 1382_retire_make_afun_2

8cefbde

edelarua merged commit a9c7d20 into main Feb 24, 2025
29 checks passed

edelarua deleted the 1382_retire_make_afun_2 branch February 24, 2025 20:39

github-actions bot locked and limited conversation to collaborators Feb 24, 2025

Melkiades reviewed Feb 25, 2025

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Retire `make_afun()` - Batch 2 #1392

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Retire make_afun() - Batch 2 #1392

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Retire `make_afun()` - Batch 2 #1392

Retire `make_afun()` - Batch 2 #1392

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